Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d5/33d436cb0b4626b87c27425a5ee7ce/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_CXK-N1-BDNA-1_B2377KTLT3_2/869_CXK-N1-BDNA-1_B2377KTLT3_2.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/foresight/xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d5/33d436cb0b4626b87c27425a5ee7ce/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_CXK-N1-BDNA-1_B2377KTLT3_2/869_CXK-N1-BDNA-1_B2377KTLT3_2.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 869_CXK-N1-BDNA-1_B2377KTLT3_2.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_CXK-N1-BDNA-1_B2377KTLT3_2.recalibrated.bam.bai
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 869_CXK-N1-BDNA-1_B2377KTLT3_2.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_CXK-N1-BDNA-1_B2377KTLT3_2.recalibrated.bam.bai
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Reads: 62615597 total, 58262 skipped (flags/unmapped)
Fragments: 31521655 total (31009902 tlen-paired, 6883 hash-paired, 5217 singletons, 5995 discordant, 493658 orphans, 6450 too large [>5000 bp], 6529631 duplicates)
Reads: 63101640 total, 53630 skipped (flags/unmapped)
Fragments: 31781453 total (31233419 tlen-paired, 7645 hash-paired, 5141 singletons, 5335 discordant, 529913 orphans, 10079 too large [>5000 bp], 6560004 duplicates)
Reads: 69108835 total, 54569 skipped (flags/unmapped)
Fragments: 34812721 total (34213660 tlen-paired, 7403 hash-paired, 5463 singletons, 4478 discordant, 581717 orphans, 8002 too large [>5000 bp], 7201528 duplicates)
Reads: 71643671 total, 93480 skipped (flags/unmapped)
Fragments: 36384862 total (34482113 tlen-paired, 7234 hash-paired, 5853 singletons, 382978 discordant, 1506684 orphans, 146502 too large [>5000 bp], 7349419 duplicates)